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- PDB-5nxz: A C145A mutant of Nesterenkonia AN1 amidase from the nitrilase su... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nxz | |||||||||
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Title | A C145A mutant of Nesterenkonia AN1 amidase from the nitrilase superfamily | |||||||||
![]() | Amidase | |||||||||
![]() | HYDROLASE / active site / amidase / cysteine 145 / alanine 145 / nitrilase superfamily | |||||||||
Function / homology | ![]() amidase / indoleacetamide hydrolase activity / N-carbamoylputrescine amidase activity / putrescine biosynthetic process from arginine / beta-alanine biosynthetic process via 3-ureidopropionate / beta-ureidopropionase activity / amidase activity Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kimani, S.W. / Sewell, B.T. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Substrate recognition by an amidase of the nitrilase superfamily Authors: Kimani, S.W. / Venter, G.A. / Sewell, B.T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.4 KB | Display | ![]() |
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PDB format | ![]() | 49.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.1 KB | Display | ![]() |
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Full document | ![]() | 424.4 KB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 20.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ny2C ![]() 5ny7C ![]() 5nybC ![]() 5nycC ![]() 5nyeC ![]() 5nz5C C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 30068.686 Da / Num. of mol.: 1 / Mutation: C145A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.75 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 2.0 M AMMONIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 6, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.21→57.49 Å / Num. obs: 82613 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 6.668 % / Biso Wilson estimate: 17.776 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.052 / Χ2: 0.948 / Net I/σ(I): 20.21 / Num. measured all: 550851 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Undeposited model Resolution: 1.21→57.49 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.2008 / WRfactor Rwork: 0.1688 / FOM work R set: 0.8772 / SU B: 0.563 / SU ML: 0.026 / SU R Cruickshank DPI: 0.0365 / SU Rfree: 0.0402 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 129.71 Å2 / Biso mean: 14.849 Å2 / Biso min: 6.55 Å2
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Refinement step | Cycle: final / Resolution: 1.21→57.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.21→1.242 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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